Sample Cohort Research Articles

Risk factors for middle ear cholesteatoma surgery based on Korean population data

Background Studies of risk factors for middle ear cholesteatoma surgery using population-based data are lacking. Objectives To investigate the risk factors for cholesteatoma surgery in adults based on population data from Korea. Materials and Methods For this retrospective study, we used Korean National Health Insurance Service National Sample Cohort data. Patients who were 20 years or older and underwent mastoidectomy from 2006 through 2015 under the diagnostic codes of cholesteatoma were defined as patients with middle ear cholesteatoma surgery. The control group was comprised of the remaining database sample in 2006. Sociodemographic factors in 2006 and histories of medical diseases, allergic diseases, and chronic sinusitis from 2003 through 2005 were compared between cholesteatoma surgery and control groups. Results A total of 459 patients underwent cholesteatoma surgery. In multivariate Cox regression analysis, age 40–59 years and residence in metropolitan cities and small- and medium-sized cities and counties were significant risk factors for cholesteatoma surgery whereas allergic rhinitis, asthma, atopic dermatitis, and chronic sinusitis were not significant risk factors for middle ear cholesteatoma surgery. Conclusions and significance The present study found no evidence of associations between allergic diseases or chronic sinusitis and cholesteatoma surgery in adults.

Protocol for the Chinese Real-World Evidence for Acute Spinal Cord Injury (ChiRES) study: a prospective, observational, multicentre cohort study of acute spinal cord injury

IntroductionSpinal cord injury (SCI) is a catastrophic event with devastating physical, social and occupational consequences for patients and their families. The number of patients with acute SCI in China continues...

Molecular Stratification and Treatment Monitoring of Lung Cancer Using a Small Extracellular Vesicle-Activated Nanocavity Architecture.

Development of molecular diagnostics for lung cancer stratification and monitoring is crucial for the rational planning and timely adjustment of treatments to improve clinical outcomes. In this regard, we propose a nanocavity architecture to sensitively profile the protein signature on small extracellular vesicles (sEVs) to enable accurate, noninvasive staging and treatment monitoring of lung cancer. The nanocavity architecture is formed by molecular recognition through the binding of sEVs with the nanobox-based core-shell surface-enhanced Raman scattering (SERS) barcodes and mirrorlike, asymmetric gold microelectrodes. By imposing an alternating current on the gold microelectrodes, a nanofluidic shear force was stimulated that supported the binding of sEVs and the efficient assembly of the nanoboxes. The binding of sEVs further induced a nanocavity between the nanobox and the gold microelectrode that significantly amplified the electromagnetic field to enable the simultaneous enhancement of Raman signals from four SERS barcodes and generate patient-specific molecular sEV signatures. Importantly, evaluated on a cohort of clinical samples (n = 76) on the nanocavity architecture, the acquired patient-specific sEV molecular signatures achieved accurate identification, stratification, and treatment monitoring of lung cancer patients, highlighting its potential for transition to clinical utility.

Multi-center evaluation of the Research Use Only NeuMoDx monkeypox virus (MPXV) fully automated real-time PCR assay.

In this manuscript, we provide detailed in silico analysis and clinical evaluation of the assay using a large cohort of clinical samples across three academic centers in Europe and the United States. Because the assay differentiates MPXV clades I and II, this manuscript is timely due to the current need to rule out the regulated clade I by diagnostic clinical laboratories. In December 2023, and due to first report of cases of sexually transmitted clade I infections in the Democratic Republic of the Congo, when generic assays that do not differentiate the clades are used, samples are considered regulated. The assay meets the need of full automation and has a marked positive impact on the laboratory workflow.

Long-term exposure to PM2.5 and mortality in a national cohort in South Korea: effect modification by community deprivation, medical infrastructure, and greenness

BackgroundLong-term exposure to PM2.5 has been linked to increased mortality risk. However, limited studies have examined the potential modifying effect of community-level characteristics on this association, particularly in Asian contexts. This study aimed to estimate the effects of long-term exposure to PM2.5 on mortality in South Korea and to examine whether community-level deprivation, medical infrastructure, and greenness modify these associations.MethodsWe conducted a nationwide cohort study using the National Health Insurance Service-National Sample Cohort. A total of 394,701 participants aged 30 years or older in 2006 were followed until 2019. Based on modelled PM2.5 concentrations, 1 to 3-year and 5-year moving averages of PM2.5 concentrations were assigned to each participant at the district level. Time-varying Cox proportional-hazards models were used to estimate the association between PM2.5 and non-accidental, circulatory, and respiratory mortality. We further conducted stratified analysis by community-level deprivation index, medical index, and normalized difference vegetation index to represent greenness.ResultsPM2.5 exposure, based on 5-year moving averages, was positively associated with non-accidental (Hazard ratio, HR: 1.10, 95% Confidence Interval, CI: 1.01, 1.20, per 10 µg/m3 increase) and circulatory mortality (HR: 1.22, 95% CI: 1.01, 1.47). The 1-year moving average of PM2.5 was associated with respiratory mortality (HR: 1.33, 95% CI: 1.05, 1.67). We observed higher associations between PM2.5 and mortality in communities with higher deprivation and limited medical infrastructure. Communities with higher greenness showed lower risk for circulatory mortality but higher risk for respiratory mortality in association with PM2.5.ConclusionsOur study found mortality effects of long-term PM2.5 exposure and underlined the role of community-level factors in modifying these association. These findings highlight the importance of considering socio-environmental contexts in the design of air quality policies to reduce health disparities and enhance overall public health outcomes.

Abstract PO5-16-01: Clinicogenomic analysis reveals genomic associations of brain metastatic tropism in breast cancer

Abstract Introduction: Recent progress in imaging and therapeutics has led to improvements in the treatment of advanced breast cancer. However, the incidence of brain metastasis (BM) in breast cancer is increasing and continues to be associated with poor prognosis and significant morbidity. Herein, we describe genomic enrichments associated with brain tropism from a large institutional clinico-genomic cohort. Methods: Patients who underwent tumor and matched normal sequencing utilizing hybridization-capture based targeted exonic sequencing (MSK-IMPACT) from April 2014 to March 2023 were included in this analysis; this cohort included 6,377 samples from 5,135 patients. We analyzed genomic data to inform the full spectrum of somatic and germline mutations, copy number changes and structural variants enriched in samples in resected BM specimens (n = 179), compared to primary tumors (n = 2980), stratified by receptor status. Enrichment analysis was conducted using a Fisher exact test for each respective receptor status. Similar analyses were conducted between extracranial metastatic (ECM) sites (n = 3186) and primary tumors, to differentiate the unique genomic features driving the emergence of BM as compared to general metastatic propensity. Multiple hypothesis testing was performed using Benjamini-Hochberg. Further genomic analysis, including allele specific copy number changes and mutational signatures will be reported at the 2023 SABCS meeting. Results: Oncogenic alterations in several genes were found to be enriched in BM samples compared to primary tumor, with an odds ratio exceeding that of the corresponding ECM comparison. For example, in the HR+/HER2- subset (4329 samples from 3476 patients), pathogenic variants in the following genes were enriched in BM:Primary analysis: NF1 (OR 6.4 [2.9 – 13.7], q = 0.001, 15.5% of BM), MYC (OR 3.9 [2.0 – 7.4], q = 0.001, 24.4% of BM), AGO2 (5.2 [2.4 – 10.9], q= 0.002, 15.5% of BM), CDKN2A (OR 3.9 [1.6 – 9.4], q = 0.06, 10.3% of BM), ERBB2 (OR 3.6 [1.5 – 8.6], q = 0.06, 10.3% of BM), RB1 (OR 4.2 [1.5 – 11.4], q = 0.06, 8.6% of BM), TP53 (OR 2.0 [1.1 – 3.5], q = 0.07, 40% of BM). In contrast, ESR1 variants were enriched in BM:Primary (OR 14.0 [6.7 – 28.2], but at the same level as ECM:Primary (OR 12.3 [8.7 – 17.7]). When considering HER2+ tumors (919 samples from 739 patients), only NKX.3 was enriched in the BM:Primary comparison (OR 11.5 [3.2 – 42.3], q = 0.004, 11.6% of BM). Although no TNBC samples met significance thresholds after adjustment for multiple hypothesis testing, CDH1, NTRK1, EGFR, and TP53 emerged as putatively significant. Conclusions: In a large cohort of genomically-profiled breast cancer samples, we find recurrent involvement of genes involved in cell cycle regulation (RB1, CDKN2A, TP53); these have been found to be enriched in brain metastases from other cancer types and are implicated in resistance to common lineage-directed therapies. Our approach also uncovered several targets for which therapies are actively in development (ERBB2, MYC). Further study of genomic evolution of breast cancer in the context of brain metastasis and therapeutic resistance will uncover conserved site-specific genomic changes and will identify novel, rational therapeutic targets. Citation Format: Anton Safonov, Deborah Smith, Emanuela Ferraro, Junchao Shen, Ishaani Khatri, Rahul Kumar, Julia An, Mark Robson, Sarat Chandarlapaty, Adrienne Boire, Nikolaus Schultz, Nelson Moss, Luke Pike, Pedram Razavi. Clinicogenomic analysis reveals genomic associations of brain metastatic tropism in breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-16-01.

Abstract PO5-13-06: Classifying HER2-low breast cancer using a combination of ERBB2 mRNA expression and altered genes

Abstract Background It has been recently demonstrated that some HER2-low, defined as immunohistochemistry (IHC) 1+ or 2+ with no gene amplification by FISH, breast cancer (BC) patients respond to trastuzumab deruxtecan (T-DXd). Results of the DAISY trial also suggested clinical activity with T-DXd in some of those classified as HER2-0 cancers by IHC, indicating an unmet need to better identify cancers that may truly respond to T-DXd. We compared ERBB2 (HER2) mRNA expression obtained from whole-transcriptome sequencing with IHC/FISH assignment of HER2 status. Furthermore, we constructed a classifier using ERBB2 expression and alterations in other genes as a proof of concept to illustrate classification of BC samples into HER2-0 versus HER2-low status. Methods We chose consecutive HR positive/HER2-negative BC samples that were submitted for OncoExTraTM testing between April 2020 and October 2022. The OncoExTra test uses tumor-normal whole exome and whole transcriptome sequencing to detect somatic single base substitutions, indels, copy number alterations, gene fusions and alternative transcripts. In addition, we investigated the expression profile of select genes for this analysis. We utilized OncoExTra data to examine the relationship between HER2 IHC status and gene expression, mutation and copy number profiles of selected genes, and built a classifier to predict HER2 status. Results A total of 279 BC samples were analyzed, including 106 HER2-IHC 0, 120 HER2-IHC 1+ and 53 HER2-IHC 2+. Of these, 273 were primary and 6 were metastatic samples. The distributions of patient age and tumor fraction were similar among these categories (p=0.54 and p=0.41, respectively; one-way ANOVA). ERBB2 expression differed among all three HER2-IHC categories and was lowest in HER2-0 and highest in HER2-2+ (HER2-0 vs HER2-1+, p< 0.001; HER2-0 vs HER2-2+, p< 0.0001; HER2-1+ vs HER2-2+, p=0.011; HER2-0 vs HER2-low, p< 0.0001; Mann-Whitney U test in all comparisons). Five genes were mutated in more than 10% of samples: PIK3CA (45.5%), GATA3 (15.4%), CDH1 (12.5%), MAP3K1 (11.1%) and TP53 (10.8%). Mutations in two genes, GATA3 and PTEN, appeared to differ in frequency between the HER2-0 and HER2-low categories (Table 1). We selected 4 genes with mutations, 2 genes with copy number changes, and expression from ERBB2, ESR1, CD274, HLA-A, HLA-B and HLA-C to train a logistic regression classifier to predict HER2 IHC status. The classifier was trained on 163 samples, hyperparameter tuning was done using 55 samples, and testing was performed on 61 samples. Preliminary results indicated that of the 28 HER2-IHC 0 samples in the test set, 17 (65%) were classified as HER2-low. Further development and evaluation of the classifier using a blinded testing set is currently in progress. Conclusion In this cohort of BC samples, ERBB2 mRNA expression was positively associated with HER2 protein IHC status. Additional studies are required to determine whether a classifier including ERBB2 mRNA expression could be used to identify patients for T-DXd therapy. The relative enrichment of PTEN alterations in HER2-IHC 0 samples suggests that mTOR/AKT inhibitors may sometimes be appropriate in patients who are not eligible for T-DXd therapy, and further investigation should be considered. Table 1. Number (frequency) of altered genes by HER2 IHC status. Citation Format: Gargi Basu, Niru Chennagiri, Turgut Dogruluk, David Hall, Jess Hoag, Cynthia Flannery, Snehal Thakkar, Melanie Palomares, Frederick Baehner, Lajos Pusztai. Classifying HER2-low breast cancer using a combination of ERBB2 mRNA expression and altered genes [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-13-06.

Abstract PO4-24-08: Genomic Landscape of Malignant Phyllodes Tumors Identifies Subsets for Targeted Therapy

Abstract Introduction: Phyllodes tumors (PT) are rare fibroepithelial tumors of the breast, comprising ~1% of all breast cancers, a subset of which have considerable malignant potential. Malignant phyllodes tumors (MPTs) have aggressive biological behavior and high local and distant recurrence rates. Distant metastases of MPTs have a poor prognosis given the limited treatment options available. Surgery remains the primary treatment modality for these patients; however, initial investigations suggest a potential for targeted therapies in managing this disease. The identification of targetable opportunities and a comprehensive understanding of the mutational profiles of MPTs could greatly enhance treatment options. Therefore, we aimed to assess the molecular landscape of these tumors. Methods: Phyllodes tumor samples underwent molecular profiling at Caris Life Sciences through DNA (592-gene panel or whole exome) and RNA sequencing (whole transcriptome). The MPTs were classified into primary and metastatic based on the specimen biopsy site. PD-L1+ expression was tested by IHC (SP142; ≥2+, ≥5%). Tumor mutational burden (TMB)-High was defined as ≥10 mutation/Mb. Immune cell fractions in the tumor microenvironment (TME) were estimated using quanTIseq (Finotello, 2019). Mann-Whitney U, Chi-square, and Fisher-Exact tests were applied where appropriate. Results: We identified 57 analyzed MPTs, all from female patients, with a median age of 53 years (range: 19-88). Approximately half of samples (53%, n=30) were labeled as from primary breast sites, and the remaining sites were metastatic (47%, n= 27). Of metastatic sites, lung was the most common location (74.1%, n=20/27), followed by bone, sacrum, pancreas and small bowel. Alterations in MPT include TERT promoter (56.8%, n=21/37), MED12 (51.6%, n=16/31), TP53 (40.0%, n=22/55), and NF1 (31.8%, n=14/44) mutations, with less frequent mutations of EGFR (10.5%, n=6/57), PIK3CA (7.0%, n=4/57), and BRAF (3.5%, n=2/57). As compared to primary MPT, metastatic MPT had roughly 2-fold higher prevalence of NF1 (45.5%: n=10/22 vs 18.2% n=4/22, p=0.05), KMT2D (25.9%: n=7/27 vs 10.7%: n=3/28, p=0.18), and RB1 (25.0%: n=6/24 vs 9.5%: n=2/21, p=0.25) though not significant. Multiple gene mutations were observed exclusively in lung metastases, as compared to non-lung sites including: TERT promoter (64.3%: n=9/14 vs 0.0%, p=0.08), MED12 (60.0%: n=6/10 vs 0.0%, p =0.044), and RB1 (35.3%: n=6/17 vs 0.0%, p=0.01). Conversely, NF1 (43.8%: n=7/16 vs 50.0%: n=3/6, p=1.0) and KMT2D (20.0%: n=4/20 vs 42.9%: n=3/7, p=0.32) mutation prevalence was higher in other metastatic sites. PD-L1+ expression was observed in 13.3% (n=7) of MPT overall, with similar prevalence among local and metastatic sites. No dMMR/MSI-H was observed, while low LOH (those with genomic LOH in < 16% of segment analyzed) was seen across MPT. Compared to a large cohort of breast adenocarcinoma samples (n=9,926) representing both HER2+ and HER2- tumors, MPT had low ERBB2 expression comparable to HER2- samples. B cells, M2 macrophages and neutrophils had the highest median cell fractions in the TME of MPT. Additionally, one MPT sample harbored a pathogenic NTRK1 fusion (TPM4:NTRK1), and treatment with larotrectinib for over 16 months suggests a clinical response to therapy. Conclusions: Our study demonstrates the importance of employing next generation sequencing (NGS) in MPTs to detect actionable genomic alterations. To effectively analyze fusions, an NGS panel that include RNA sequencing is recommended, considering the occurrence of NTRK1 fusion reported herein. Although HER2 transcriptional expression was low, further investigations examining HER2 IHC in PTs are still necessary. These finding therefore highlight the importance of NGS in phyllodes tumors research, as it may uncover potential targeted treatment options for patients. Citation Format: Rani Bansal, Tolulope Adeyelu, Andrew Elliott, Antoinette Tan, Jane Meisel, Matthew Oberley, Stephanie Graff, Jorge Reis-Filho, George Sledge Jr, Sarah Sammons, Laura Rosenberger. Genomic Landscape of Malignant Phyllodes Tumors Identifies Subsets for Targeted Therapy [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-24-08.

Abstract PO1-03-09: Transcriptomic profiling of ER-negative and ER-low, HER2-negative breast cancer and its implications on immune regulation

Abstract Background: The recommended cut-off of < 1% positive cells to define estrogen receptor (ER) negative status in breast cancer (BC) is highly debated. Few data exist on transcriptomic features of ER-low BC, suggesting no major differences vs ER-neg. Among HER2-negative BCs, we compared gene-expression profiling (including PAM50 intrinsic subtyping) according to ER status (ER-neg: 0% vs. ER-low: 1-9%) and assessed its impact on Tumor-infiltrating lymphocytes (TILs) levels. Methods: Across two cancer centers, stage I-III HER2-negative BCs FFPE samples were reviewed for ER status. All ER-low (ER 1-9%) samples were identified and a cohort of ER-neg BC samples, matched for age and stage, was also retrieved. A small cohort of pts with intermediate ER expression (ER-int: 10-50%) was included as a control cohort. Expression of 776 BC–related genes was evaluated by nCounter® (Breast Cancer 360TM Panel) and intrinsic molecular subtyping was determined using the PAM50 subtype predictor. A False Discovery Rate (FDR) corrected unpaired two-class SAM was used to identify genes differentially expressed in different subgroups. TILs were evaluated on archival H&E slides following guidelines. Results: Of 116 stage I-III HER2-neg BC pts included, 39 had ER-neg BC, 65 had ER-low BC, and 12 had ER-int disease. PAM50 intrinsic subtype distribution was similar in ER-neg and ER-low BCs, (with an enrichment in basal-like tumors), while both subgroups differed significantly from ER-int samples (Table). As compared to ER-neg tumors, ER-low BCs showed significantly higher expression of GATA3 gene and lower expression of EDN1 and PROM1 genes by SAM analysis (FDR< 5%); however, when the analysis was limited to PAM50 basal-like tumors (N=77) we only identified two genes that were downregulated in ER-low BCs (EDN1, PROM1) as compared to ER-neg BCs. On the contrary, significant differences in transcriptomic regulation were observed between ER-low and ER-int BCs, with ER-low BCs showing significantly higher expression of 53 genes and lower expression of 398 genes, as compared to ER-int (SAM analysis FDR< 5%). We previously reported similar TIL levels in ER-low and ER-neg tumors. In both ER-low and ER-int BCs, PAM50 basal-like subtype was associated with significantly higher TILs: median TIL levels 20 (range 0-80) and 6 (range 1-40) for PAM50 Basal-like BCs versus other PAM50 subtypes respectively in ER-low samples (p< 0.001); median TIL levels 53 (range 25-80) and 5 (range 0-10) for PAM50 Basal-like BCs versus other PAM50 subtypes respectively in ER-int samples (p=0.036). No significant difference in TIL levels according to PAM50 subtyping were observed in ER-neg tumors. No significant difference in mRNA levels for PD-1 (PDCD1) and PD-L1 (CD274) genes was observed between ER-low and ER-neg tumors. Conclusions: Among patients with HER2-neg BC, gene-expression profiling is similar in ER-neg (i.e., < 1%) vs. ER-low tumors with a high prevalence of PAM50 Basal-like tumors and few differentially expressed genes. In both ER-low and ER-int HER2-neg BCs, PAM50 Basal-like subtype is also associated with higher TIL levels. Our results strongly indicate that HER2-neg/ER-low BCs and HER2-neg/ER-neg BCs are similar biological entities, thus further supporting the use of similar treatments in patients with early-stage ER-low and triple-negative BC, including immune checkpoint inhibitors. PAM50 intrinsic subtype distribution according to ER levels Citation Format: Gaia Griguolo, Claudio Vernieri, Davide Massa, Lorenzo Nicolè, Claudia Pinato, Federica Miglietta, Andrea Vingiani, Silvia Brich, Riccardo Lobefaro, Francesca Schiavi, Matteo Fassan, Giancarlo Pruneri, Valentina Guarneri, Maria Vittoria Dieci. Transcriptomic profiling of ER-negative and ER-low, HER2-negative breast cancer and its implications on immune regulation [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-03-09.

Abstract PO3-26-07: Epigenetic approaches to deliver a targeted radiotherapy for triple negative breast cancer

Abstract The sodium iodide symporter (NIS, encoded by SLC5A5) is the sole transporter of iodide, and successfully exploited in thyroid cancer to uptake radioiodide (RAI). NIS is essentially undetected in normal mammary epithelial cells but elevated during lactation, and has a heterogeneous expression profile in breast cancer (BRCA), as evidenced by TCGA cohort and also in a ~120 sample TMA we have profiled. Furthermore, pre-clinical studies support an epigenetic mechanisms that involves Retinoic Acid Receptor alpha (RARa) to regulate SLC5A5 expression. Therefore, we have applied an orthogonal approach to both elucidate and target mechanisms that control NIS expression and function to deliver a therapeutic strategy that targets this transporter as a novel radiotherapy in BRCA. To understand the epigenetic control of expression we segregated samples in the TCGA-BRCA cohort into lower and upper quartile SLC5A5 expression and identified ~600 significant differentially expressed of genes (DEG). Interestingly, restricting analyses to either triple negative (TN) or tumors from African American (AA) patients doubled the number of DEGs. These DEGs were significantly associated with several transcription factors including LHX3, a pituitary development transcription factor regulated by thyroid signaling. The most significantly altered ~70 DEGs significantly clustered tumors by genomic ancestry and ERBB2/HER2 IHC status. The DEGs also supported a footprint of RARa signaling include PRAME, a known RARa co-repressor associated with histone deacetylase, and reflects the finding that NIS expression is highly responsive to SAHA treatment. To investigate if PRAME expression suppresses RARa regulation of SLC5A5 we have established a panel of BRCA cell lines (AU565, SKB3 SUM52 and MDA-MB-231) stably transfected with either CRISPR-VP64 (activator) and CRISPR-KRAB (repressor) to modulate PRAME and measure the epigenomic impact, the expression of SLC5A5 and the ability to transport RAI. In parallel we have applied a drug screen approach that targets non-canonical approaches to govern NIS expression, for example by targeting valosin-containing protein (VCP) that induces NIS proteolysis. In the first instance we have developed a therapeutic strategy to target NIS by inhibiting VCP. Specifically, we are screening a range of VCP inhibitors in combination with the HDAC inhibitor SAHA or the transcriptional potentiator, disulfiram metabolite Cu(DDC)2 in BRCA cell lines by testing the ability to augment RAI uptake. Remarkably, in MDA MB 231 cells, Cu(DDC)2 combined with the VCP inhibitor CB5339, resulted in a significant additive increase in RAI uptake and a prominent decrease in cell proliferation and survival. These studies combined with future murine and PDX testing of CRISPR-edited tumors and drug exposures will develop a comprehensive analyses of the mechanisms that control SLC5A5 expression across breast cancer cell types, how this can be most effectively targeted to restore NIS expression, and exploited to promote RAI as a novel targeted BRCA radiotherapy. Citation Format: Katie Brookes, Martin Read, Sajad Wani, Sissy Jhiang, Daniel Stover, Mathew Ringel, Christopher McCabe, Moray Campbell. Epigenetic approaches to deliver a targeted radiotherapy for triple negative breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-26-07.

Appendectomy and the Risk of Parkinson's Disease: A Korean Nationwide Study.

The vermiform appendix is considered a potential reservoir for the abnormal α-synuclein aggregate in Parkinson's disease (PD). Previous epidemiologic evidence on the association between appendectomy and PD risk remains inconclusive, especially outside the Western world. To investigate the association between appendectomy and PD risk in Korea. Among 703,831 eligible adult subjects in the National Health Insurance Service sample cohort, we identified 16,122 patients who underwent appendectomy. The rest formed the control group. PD risk was assessed using time-dependent Cox regression analyses. The appendectomy group did not have altered risk of PD compared with the control group in either unadjusted [hazard ratio (HR) 1.32, 95% confidence interval (CI) 0.97-1.80, P = 0.08] or adjusted model (HR 1.42, CI 0.88-2.30, P = 0.15). No further statistical difference appeared when stratified by sex. Appendectomy is not associated with altered risk of PD in the Korean population.

Abstract PO2-28-09: Long-term Breast Cancer Risk Prediction in Black Women: External Validation of a Mammography-driven AI Model

Abstract Despite the demonstrated potential of artificial intelligence (AI) in breast cancer risk assessment for personalizing screening recommendations, further validation is required regarding AI model bias and generalizability. We performed external validation in Black women of a mammography-driven AI breast cancer risk model (Mirai) originally developed on screening cohorts primarily consisting of White women. In this institutional review board-approved, Health Insurance Portability and Protection Act (HIPAA)-compliant study under a waiver of consent, we retrospectively analyzed a case–cohort sample nested within the core academic breast cancer screening practice of BJC Healthcare, the hospital partner of Washington University in St. Louis. For the purposes of this validation study, relying on 2D digital mammography (DM) images, we focused on Black women presenting for annual DM screening (Selenia or Selenia Dimensions; Hologic) between 2008 and 2018. Eligible breast cancer cases were derived from all women with a breast cancer diagnosis (with associated biopsy-confirmed tumor pathology via institutional cancer registry) after negative (BI-RADS 1 or 2) DM screening 1 to 5 years prior to cancer diagnosis. We also identified a random sample of controls, defined as women who had negative (BI-RADS 1 or 2) DM screening, with 1 to 5 years of screening follow-up without a cancer diagnosis. Risk scores for all DM exams were calculated via the Mirai model. Performance was evaluated using concordance-index (C) analyses and associated 95% confidence intervals (CIs) for the entire cohort, as well as for study subgroups of invasive versus in-situ cancer and cancer molecular subtypes. We analyzed 1368 DM screening exams, including 672 DM exams from 391 women diagnosed with breast cancer (mean age, 58 years; standard deviation, 10 years) and 696 DM exams from 406 controls (mean age, 55 years; standard deviation, 10 years). The overall C-index was 0.62 [95% CIs 0.60–0.64] for all Black women, which was lower compared to previously reported validation results for Mirai in studies of similar design on predominantly White and racially diverse screening cohorts (C-index = 0.67-0.78). There was no evidence of a significant difference between invasive and in-situ cancer (C-index = 0.64 [95% CIs 0.61–0.66] vs. 0.64 [95% CIs 0.61–0.67]). Compared to other cancer molecular subtypes, performance was significantly higher among triple-negative (C-index = 0.67 [95% CIs 0.62–0.71]) and estrogen receptor (ER) negative cancer (C-index = 0.66 [95% CIs 0.61–0.70]). A previously developed mammography-driven AI model showed overall good performance in long-term breast cancer risk assessment in a dataset of Black women only, particularly for triple-negative and ER- cancer types. However, performance was lower compared to previously reported validation results from similar studies on predominantly White and racially diverse screening cohorts. Our results suggest that further refinements are needed towards more accurate breast cancer risk assessment in Black women. Long-term breast cancer risk prediction performance (C-indices) of Mirai in the full cohort of Black women and in study subgroups. Citation Format: Juanita Hernandez Lopez, Zhixin Sun, Shirin Shoushtari, Ulugbek Kamilov, Debbie Bennett, Aimilia Gastounioti. Long-term Breast Cancer Risk Prediction in Black Women: External Validation of a Mammography-driven AI Model [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-28-09.

Abstract PO4-18-01: International Validation of a Staging Model for de novo Metastatic Breast Cancer

Abstract Background Given the heterogeneity in outcomes for de novo metastatic breast cancer (dnMBC), a staging system was recently developed that refines prognostic estimates for patients presenting with distant metastases (JCO 2023;10:2546). This staging model was developed using the National Cancer Database and stratified patients into 4 subgroups, termed IVA, IVB, IVC, and IVD based on 3-year overall survival (OS): IVA >70%, IVB 50-70%, IVC 25-< 50%, and IVD < 25%; the primary factors affecting higher stage grouping were negative for ER, PR, and HER2 expression and a higher number of involved organ sites. Here, we aim to validate this model using an international data set. Methods Data for dnMBC patients were obtained from the Netherlands Cancer Registry (NCR, hosted by IKNL), Epidemiological Strategy and Medical Economics (ESME) by Unicancer, British Columbia Cancer (BCCan), Instituto Nacional de Cancerología, México (INCan), and Grupo Español de Investigación en Cáncer de Mama (GEICAM); the diagnosis years included varied by organization (range 2002-2021). Stage groups were assigned based on previously published criteria, defined by T-category, grade, ER, PR, HER2, histology, organ system site of metastases (bone-only, brain-only, visceral), and number of organ systems involved. For each cohort, followup time and OS were estimated using the reverse Kapan-Meier and Kaplan-Meier method, respectively. Median rates were estimated across all cohorts by weighting on cohort sample size or number at risk. Cox proportional hazards models were used to estimate the association of stage with OS after adjustment for age at diagnosis (treatment data not available for all cohorts). For the ESME cohort, a subgroup multivariable analysis was used to estimate the association of stage with OS after adjustment for age, local (surgery or radiotherapy) and first line systemic treatments. Results The final validation cohort was comprised of N=11,199 patients from 5 international organizations: n=5063 (45.2%, IKNL), n=4139 (37.0%, ESME), n=774 (6.9%, BCCan), n=757 (6.8%, INCan), and n=466 (4.2% GEICAM). Median followup across all cohorts was 77.5 months (95% CI 74.3-80.2). Median followup (in months) for the IKNL, ESME, BCCan, INCan, and GEICAM cohorts was 45.3 (95% CI 43.6-47.1), 77.5 (95% CI 74.3-80.2), 105.0 (95% CI 95.9-106.5), 93.0 (95% CI 86.5-102.1), and 49.5 (95% CI 46.5-53.4), respectively. Patients were stratified into stage groups: IVA, n=603 (5.4%); IVB, n=5704 (50.9%); IVC, n=3356 (30.0%); IVD, n=1536 (13.7%). For all cohorts combined, the weighted average OS rates consistently decreased with increasing stage group; similar findings were noted for individual cohorts (all p< 0.001; Table). On multivariable subgroup analysis including age at diagnosis, stage group was significantly associated with OS, and the risk of death increased with increasing stage (all p< 0.001; Table). On multivariable subgroup analysis for n=4139 patients (ESME cohort), stage group remained significantly associated with OS [IVA: reference; IVB: HR 1.51 (95% CI 1.17-1.93); IVC: HR 2.11 (95% CI 1.64-2.72); IVD: HR 3.60 (95% CI 2.75-4.70)] after adjusting for age and treatment. Conclusions These findings provide external validation of the previously published staging guidelines for dnMBC. This may guide future revisions of the AJCC staging guidelines for patients with dnMBC and provide patients and providers valuable information in planning therapy and goals of care as they approach the end-of-life. Table. Citation Format: Jennifer Plichta, Samantha Thomas, Sabine Siesling, Linda de Munck, Amélie Lusque, Thomas Grinda, Lovedeep Gondara, Stephen Chia, Paula Cabrera-Galeana, Nancy Reynoso-Noverón, Sara López-Tarruella, Isabel Álvarez López, Stephen Edge, Gabriel Hortobagyi. International Validation of a Staging Model for de novo Metastatic Breast Cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-18-01.

Predicting hematoma expansion using machine learning: An exploratory analysis of the ATACH 2 trial

IntroductionHematoma expansion (HE) in patients with intracerebral hemorrhage (ICH) is a key predictor of poor prognosis and potentially amenable to treatment. This study aimed to build a classification model to predict HE in patients with ICH using deep learning algorithms without using advanced radiological features. MethodsData from the ATACH-2 trial (Antihypertensive Treatment of Acute Cerebral Hemorrhage) was utilized. Variables included in the models were chosen as per literature consensus on salient variables associated with HE. HE was defined as increase in either >33% or 6 mL in hematoma volume in the first 24 h. Multiple machine learning algorithms were employed using iterative feature selection and outcome balancing methods. 70% of patients were used for training and 30% for internal validation. We compared the ML models to a logistic regression model and calculated AUC, accuracy, sensitivity and specificity for the internal validation models respective models. ResultsAmong 1000 patients included in the ATACH-2 trial, 924 had the complete parameters which were included in the analytical cohort. The median [interquartile range (IQR)] initial hematoma volume was 9.93.mm3 [5.03–18.17] and 25.2% had HE. The best performing model across all feature selection groups and sampling cohorts was using an artificial neural network (ANN) for HE in the testing cohort with AUC 0.702 [95% CI, 0.631–0.774] with 8 hidden layer nodes The traditional logistic regression yielded AUC 0.658 [95% CI, 0.641–0.675]. All other models performed with less accuracy and lower AUC. Initial hematoma volume, time to initial CT head, and initial SBP emerged as most relevant variables across all best performing models. ConclusionWe developed multiple ML algorithms to predict HE with the ANN classifying the best without advanced radiographic features, although the AUC was only modestly better than other models. A larger, more heterogenous dataset is needed to further build and better generalize the models.

Comparison of Novel Proteomic Expression Profiles for Radiation Exposure in Male and Female C57BL6 Mice.

There is a need for point-of-care diagnostics for future mass casualty events involving radiation exposure. The development of radiation exposure and dose prediction algorithms for biodosimetry is needed for screening of large populations during these scenarios, and exploration of the potential effects which sex, age, genetic heterogeneity, and physiological comorbidities may have on the utility of biodosimetry diagnostics is needed. In the current study, proteomic profiling was used to examine sex-specific differences in age-matched C57BL6 mice on the blood proteome after radiation exposure, and the usefulness of development and application of biodosimetry algorithms using both male and female samples. Male and female mice between 9-11 weeks of age received a dose of total-body irradiation (TBI) of either 2, 4 or 8 Gy and plasma was collected at days 1, 3 and 7 postirradiation. Plasma was then screened using the SomaScan v4.1 assay for ∼7,000 protein analytes. A subset panel of protein biomarkers demonstrated significant (FDR < 0.05 and |logFC| > 0.2) changes in expression after radiation exposure. All proteins were used for feature selection to build predictive models of radiation exposure using different sample and sex-specific cohorts. Both binary (prediction of any radiation exposure) and multidose (prediction of specific radiation dose) model series were developed using either female and male samples combined or only female or only male samples. The binary series (models 1, 2 and 3) and multidose series (models 4, 5 and 6) included female/male combined, female only and male only respectively. Detectable values were obtained for all ∼7,000 proteins included in the SomaScan assay for all samples. Each model algorithm built using a unique sample cohort was validated with a training set of samples and tested with a separate new sample series. Overall predictive accuracies in the binary model series was ∼100% at the model training level, and when tested with fresh samples, 97.9% for model 1 (female and male) and 100% for model 2 (female only) and model 3 (male only). When sex-specific models 2 and 3 were tested with the opposite sex, the overall predictive accuracy rate dropped to 62.5% for model 2 and remained 100% for model 3. The overall predictive accuracy rate in the multidose model series was 100% for all models at the model training level and, when tested with fresh samples, 83.3%, 75% and 83.3% for Multidose models 4-6, respectively. When sex-specific model 5 (female only) and model 6 (male only) were tested with the opposite sex, the overall predictive accuracy rate dropped to 52.1% and 68.8%, respectively. These models represent novel predictive panels of radiation-responsive proteomic biomarkers and illustrate the utility and necessity of considering sex-specific differences in development of radiation biodosimetry prediction algorithms. As sex-specific differences were observed in this study, and as use of point-of-care radiation diagnostics in future mass casualty settings will necessarily include persons of both sexes, consideration of sex-specific variation is essential to ensure these diagnostic tools have practical utility in the field.

MIR4435-2HG as a possible novel predictive biomarker of chemotherapy response and death in pediatric B-cell ALL.

Introduction: Although B-cell acute lymphoblastic leukemia (B-cell ALL) survival rates have improved in recent years, Hispanic children continue to have poorer survival rates. There are few tools available to identify at the time of diagnosis whether the patient will respond to induction therapy. Our goal was to identify predictive biomarkers of treatment response, which could also serve as prognostic biomarkers of death, by identifying methylated and differentially expressed genes between patients with positive minimal residual disease (MRD+) and negative minimal residual disease (MRD-). Methods: DNA and RNA were extracted from tumor blasts separated by immunomagnetic columns. Illumina MethlationEPIC and mRNA sequencing assays were performed on 13 bone marrows from Hispanic children with B-cell ALL. Partek Flow was used for transcript mapping and quantification, followed by differential expression analysis using DEseq2. DNA methylation analyses were performed with Partek Genomic Suite and Genome Studio. Gene expression and differential methylation were compared between patients with MRD-/- and MRD+/+ at the end of induction chemotherapy. Overexpressed and hypomethylated genes were selected and validated by RT-qPCR in samples of an independent validation cohort. The predictive ability of the genes was assessed by logistic regression. Survival and Cox regression analyses were performed to determine the association of genes with death. Results: DAPK1, BOC, CNKSR3, MIR4435-2HG, CTHRC1, NPDC1, SLC45A3, ITGA6, and ASCL2 were overexpressed and hypomethylated in MRD+/+ patients. Overexpression was also validated by RT-qPCR. DAPK1, BOC, ASCL2, and CNKSR3 can predict refractoriness, but MIR4435-2HG is the best predictor. Additionally, higher expression of MIR4435-2HG increases the probability of non-response, death, and the risk of death. Finally, MIR4435-2HG overexpression, together with MRD+, are associated with poorer survival, and together with overexpression of DAPK1 and ASCL2, it could improve the risk classification of patients with normal karyotype. Conclusion: MIR4435-2HG is a potential predictive biomarker of treatment response and death in children with B-cell ALL.

Discovery and Verification of Sjögren's Syndrome Protein Biomarkers in Tears by Targeted LC-MRM.

Sjögren's syndrome (SS) is an autoimmune rheumatic disorder characterized by exocrine gland dysfunction, mainly from the lacrimal and salivary glands. The disease causes severe aqueous dry eye syndrome (DED) and is associated with high rates of complications, including corneal ulceration, scaring, and perforation. Systemic complications may occur as well as a higher risk of developing lymphoma. Diagnosis of SS-DED is often delayed and difficult to establish. With the aim of discovering biomarkers to help discriminate SS-DED patients, a combination of untargeted and targeted LC-MS/MS analyses were performed on tear samples collected on Schirmer strips and subjected to tryptic digestion. Following the analysis of three cohorts and the development of two targeted LC-sMRM methods for the verification of putative biomarkers found in the first cohort of samples, 64 proteins could be linked to Sjögren's syndrome, in the hopes of helping to confirm diagnoses as well as potentially stratifying the severity of disease in these patients. Proteins that were increased in SS-DED showed activation of the immune system and alterations in homeostasis. Several proteases and protease inhibitors were found to be significantly changing in SS-DED, as well as a consistent decrease in specific proteins known to be secreted by the lacrimal gland.

The oxytocin antagonist cligosiban reduces human prostate contractility: Implications for the treatment of benign prostatic hyperplasia.

With increasing life expectancy, benign prostatic hyperplasia (BPH) consequently affects more ageing men, illustrating the urgent need for advancements in BPH therapy. One emerging possibility may be the use of oxytocin antagonists to relax smooth muscle cells in the prostate, similar to the currently used (although often associated with side effects) α1-adrenoceptor blockers. For the first time we used live-imaging, combined with a novel image analysis method, to investigate the multidirectional contractions of the human prostate and determine their changes in response to oxytocin and the oxytocin antagonists atosiban and cligosiban. Human prostate samples were obtained and compared from patients undergoing prostatectomy due to prostate cancer as well as from patients with transurethral resection of prostate tissue due to severe BPH. The two cohorts of tissue samples showed spontaneous multidirectional contractions, which significantly increased after the addition of oxytocin. Different to atosiban, which showed ambiguous effects of short duration, only long-acting cligosiban reliably prevented, as well as counteracted, any contractile oxytocin effect. Furthermore, cligosiban visibly reduced not only oxytocin-induced contractions, but also showed intrinsic activity to relax prostatic tissue. Thus, the oxytocin antagonist cligosiban could be an interesting candidate in the search for novel BPH treatment options.

A role for vessel-associated extracellular matrix proteins in multiple sclerosis pathology.

Multiple sclerosis (MS) is unsurpassed for its clinical and pathological hetherogeneity, but the biological determinants of this variability are unknown. HLA-DRB1*15, the main genetic risk factor for MS, influences the severity and distribution of MS pathology. This study set out to unravel the molecular determinants of the heterogeneity of MS pathology in relation to HLA-DRB1*15 status. Shotgun proteomics from a discovery cohort of MS spinal cord samples segregated by HLA-DRB*15 status revealed overexpression of the extracellular matrix (ECM) proteins, biglycan, decorin, and prolargin in HLA-DRB*15-positive cases, adding to established literature on a role of ECM proteins in MS pathology that has heretofore lacked systematic pathological validation. These findings informed a neuropathological characterisation of these proteins in a large autopsy cohort of 41 MS cases (18 HLA-DRB1*15-positive and 23 HLA-DRB1*15-negative), and seven non-neurological controls on motor cortical, cervical and lumbar spinal cord tissue. Biglycan and decorin demonstrate a striking perivascular expression pattern in controls that is reduced in MS (-36.5%, p = 0.036 and - 24.7%, p = 0.039; respectively) in lesional and non-lesional areas. A concomitant increase in diffuse parenchymal accumulation of biglycan and decorin is seen in MS (p = 0.015 and p = 0.001, respectively), particularly in HLA-DRB1*15-positive cases (p = 0.007 and p = 0.046, respectively). Prolargin shows a faint parenchymal pattern in controls that is markedly increased in MS cases where a perivascular deposition pattern is observed (motor cortex +97.5%, p = 0.001; cervical cord +49.1%, p = 0.016). Our findings point to ECM proteins and the vascular interface playing a central role in MS pathology within and outside the plaque area. As ECM proteins are known potent pro-inflammatory molecules, their parenchymal accumulation may contribute to disease severity. This study brings to light novel factors that may contribute to the heterogeneity of the topographical variation of MS pathology.

Seasonal variability in the otolith and somatic size relationship of Japanese anchovy larvae: Counter effects of somatic growth and temperature

Otolith microstructure analysis has played an essential role in understanding the recruitment mechanisms of fish. Despite the fundamental assumption of a close correlation between otolith size and somatic size in growth back-calculations, numerous studies have shown that somatic growth and temperature have negative and positive effects on otolith size at the same somatic size, respectively. However, few studies have investigated the effects of somatic growth and temperature on otolith and somatic size relationships at intra- and inter-cohort levels in the same study framework. The present study investigated the effects of somatic growth and temperature on the seasonal variability in the otolith and somatic size relationship in Japanese anchovy Engraulis japonicus larvae collected from multiple seasonal cohorts throughout the year in the Kii Channel, Japan. The otolith and somatic size relationships were strong within each seasonal cohort sample (R2 = 0.771–0.949), but the relationship became weaker when all the seasonal data were pooled (R2 = 0.571). Relative otolith size at a given somatic size (ROS) was negatively related to somatic growth rates within each seasonal cohort sample (i.e., at the intra-cohort level), but the relationship became weak when all the data were pooled. On the contrary, sea temperature had positive effects on ROS, which would explain the seasonal variability in the otolith and somatic size relationship. The multiple regression analysis showed that temperature influenced ROS almost six times more than somatic growth. Overall, the present study demonstrated that an uncoupling in the otolith size–somatic size relationship was generated by the counter effects of somatic growth and temperature. The observed counter effects should be taken into account in estimating past larval growth for larvae obtained from different environmental conditions.